Hello, The output model of modeller has the postfix .B99990001 and not .atm The postfix .atm symboles a file in a pdb format.

The script model-default.top has a few lines that refer to the input it should get: 1. ALNFILE must be equal to the name of your input alignmnet. 2. KNOWNS must be equal to the name of your template for example for the template pdb1awi.ent you must write 1awi. 3. SEQUENCE must be equal to the name of the query as it appears on the alignment. 4. ATOM_FILES_DIRECTORY must be equal to the directory where you hold your template files.

I hope this will help you, Iris.

On Thu, 17 Oct 2002, Somanadh Babu wrote:

> Hello, > I am a begiiner with modeller. > I am using modeller6v2. I tried running modeller with model-default.top as > the input file and from what I knew,a '.atm' file has to be generated after > the process. I am working in LINUX. > The process stopped after a couple of seconds and the message STOP was > thrown. No ".atm" file was generated. How do I proceed further? > sincerely, > somanadh >